Studies conducted in developing countries have noted associations between concurrent stunting, social-emotional problems and poor cognitive ability in young children. However, the relative contribution of these variables in Latin America is likely changing as undernutrition rates decline and prevalence of childhood obesity rises. We conducted a cross-sectional study of 106 normal-weight and 109 obese preschool children to compare the relative contribution of early nutrition, sociodemographic factors and psychosocial variables on cognitive development in normal-weight and obese preschool children in Chile. The study variables were categorized as: (1) socio-demographic (age, sex, birth order and socioeconomic) (2) early nutrition (maternal height, birth weight, birth length and height at 5 years) (3) psychosocial factors (maternal depression, social-emotional wellbeing and home space sufficiency). In order to assess determinants of cognitive development at 4-5 years we measured intelligence quotient (IQ); variability in normal children was mostly explained by socio-demographic characteristics (r(2) = 0.26), while in obese children early nutritional factors had a significant effect (r(2) = 0.12) beyond socio-demographic factors (r(2) = 0.19). Normal-weight children, who were first born, of slightly better SES and height Z score >1, had an IQ ≥ 6 points greater than their counterparts (p < 0.05). Obese children who were first born with birth weight >4,000 g and low risk of socio-emotional problems had on average ≥5 IQ points greater than their peers (p < 0.05). We conclude that in Chile, a post-transitional country, IQ variability of normal children was mostly explained by socio-demographic characteristics; while in obese children, early nutrition also played a significant role.